There's a bunch of micro brands that take movements from ETA/Sellita/etc, cases from Fricker/etc, and then do their own dials, crystals and other modifications. Some also have custom cases, but the price tends to creep up.
Here's a few examples that have a good reputation:
Christopher Ward
http://www.christopherward-usa.com (I like their GMTs)
Steinhart
http://www.steinhartwatches.de/en/
MKII
http://www.mkiiwatches.com (noted for extremly long ordering times, but beautifully crafted)
Karl.